Variant report

Variant	rs10052879
Chromosome Location	chr5:118555242-118555243
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:118553070..118555553-chr5:118571329..118573313,2	K562	blood:

Variant related genes	Relation type
ENSG00000172869	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10064311	1.00[JPT][hapmap]
rs10071407	1.00[JPT][hapmap]
rs10900727	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs11241498	0.90[ASN][1000 genomes]
rs12653870	0.87[CHD][hapmap]
rs1394629	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2404395	0.85[ASN][1000 genomes]
rs4286709	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4380699	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4512152	0.85[CEU][hapmap]
rs4583917	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4895185	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs61279074	0.85[ASN][1000 genomes]
rs6595174	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap]
rs6595178	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6595179	0.95[ASN][1000 genomes]
rs6863826	0.87[CHD][hapmap];0.80[GIH][hapmap]
rs6874843	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6880622	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.90[ASN][1000 genomes]
rs6889308	1.00[JPT][hapmap]
rs7702867	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[ASN][1000 genomes]
rs7720231	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.86[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7734532	1.00[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9327087	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9327093	1.00[JPT][hapmap]
rs9790885	0.87[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462426	chr5:118465249-118621672	Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv599564	chr5:118465249-118621672	ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1016595	chr5:118468658-118621672	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1019788	chr5:118488501-118607405	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv537882	chr5:118488501-118607405	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1034616	chr5:118506348-118600391	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv1031914	chr5:118516878-118589497	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118485800-118572200	Weak transcription	Small Intestine	intestine
2	chr5:118486000-118588600	Weak transcription	Right Ventricle	heart
3	chr5:118489800-118591200	Weak transcription	Colonic Mucosa	Colon
4	chr5:118498000-118584200	Weak transcription	Spleen	Spleen
5	chr5:118503800-118585800	Weak transcription	NH-A	brain
6	chr5:118507800-118580200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr5:118514400-118589000	Weak transcription	Pancreas	Pancrea
8	chr5:118514400-118591400	Weak transcription	Esophagus	oesophagus
9	chr5:118521200-118571000	Weak transcription	HMEC	breast
10	chr5:118524200-118570800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr5:118524400-118571000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr5:118524600-118561200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr5:118524600-118584200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr5:118534600-118574200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr5:118535000-118560800	Weak transcription	Gastric	stomach
16	chr5:118535000-118579600	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr5:118535000-118584800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr5:118535000-118587400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr5:118535000-118588200	Weak transcription	Lung	lung
20	chr5:118535000-118589000	Weak transcription	Aorta	Aorta
21	chr5:118535200-118555600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr5:118535200-118575200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr5:118535400-118555400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr5:118535400-118569400	Weak transcription	Thymus	Thymus
25	chr5:118535600-118555800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr5:118536400-118556000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr5:118536400-118556200	Weak transcription	Stomach Smooth Muscle	stomach
28	chr5:118536400-118569800	Weak transcription	Brain Angular Gyrus	brain
29	chr5:118536400-118580000	Weak transcription	Fetal Brain Male	brain
30	chr5:118538200-118562000	Weak transcription	Brain Germinal Matrix	brain
31	chr5:118538200-118569000	Weak transcription	Ovary	ovary
32	chr5:118538200-118569400	Weak transcription	Fetal Brain Female	brain
33	chr5:118538200-118581800	Weak transcription	Brain Hippocampus Middle	brain
34	chr5:118538200-118586600	Weak transcription	Brain Substantia Nigra	brain
35	chr5:118538200-118590600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr5:118539200-118580800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr5:118539200-118581600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr5:118539200-118590000	Weak transcription	Fetal Kidney	kidney
39	chr5:118539200-118591000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr5:118539400-118556000	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr5:118539400-118556000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr5:118539400-118556200	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr5:118539400-118570600	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr5:118540000-118569800	Weak transcription	Fetal Lung	lung
45	chr5:118540200-118555600	Weak transcription	Fetal Thymus	thymus
46	chr5:118540200-118557600	Weak transcription	Placenta	Placenta
47	chr5:118540200-118563200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr5:118540200-118569600	Weak transcription	Fetal Muscle Trunk	muscle
49	chr5:118540400-118558200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr5:118540600-118555400	Weak transcription	Fetal Intestine Large	intestine

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